Identification of functional variants can be viewed as the end-game of genetic analysis or the starting point to understand roles of genes in behaviors. Public databases are populated with >20 million sequence variants, mostly single nucleotide polymorphisms. However, most rare and uncommon variants are unknown, and functionality of most is unknown. We discovered polymorphisms in >50 neurogenetic candidate genes. Several alter function of the encoded protein, or gene expression. A rare, gain-of-function serotonin transporter variant Ile425Val may lead to severe pathology including Asperger's syndrome, treatment resistant OCD, and anorexia nervosa, in two families in which it is segregating. In the promoter region of this gene the HTTLPR polymorphism alters transcription. At HTTLPR we described a common, functional allele (LA->LG)(Hu et al) enhancing linkage studies to behavioral phenotypes and intermediate phenotypes. HTTLPR was linked to SSRI treatment response of depressed patients, via treatment tolerability (Hu et al, 2007). Common HTR2C Ser23Cys and HTR2A Asn452His alleles were detected, shown to be functional and linked by others to clozapine responsive of schizophrenics. In first-episode schizophrenics, we helped show that a functional DRD2 promoter polymorphism influences antipsychotic response (Lencz et al, 2006). We detected a OPRM1 Asn40Asp missense variant (Bergen et al) that was shown by others to be functional and linked by others, and later by us (Anton et al, 2008), to naltrexone treatment response in alcoholics. Recently we traced linkages of NPY (Zhu et al, 2008), GCH1 (Tegeder et al) and DISC1 (Hodgkinson et al) to behavior to functional haplotypes and alleles. By deep sequencing 14 genes involved in dopamine and serotonin function we found a Stop codon that is relatively common in the Finnish population, and both associated with impulsive behavior and cosegregating with impulsive behavior in families. The association we found between a low expression Neuropeptide Y (NPY) haplotype and increased anxiety and emotionality illustrates effects of functional genetic variation on multiple levels of brain function and on complex behavior. Genetically determined reduction of expression of this anxiolytic neuropeptide predicted reduced trait anxiety and liability to anxiety disorders and increased responses to emotional stimuli as shown by fMRI and to pain/stress as shown by carfentanil PET (Zhou et al, Nature, 2008). We created a 1536 SNP Addictions Array enabling haplotype-based and candidate locus coverage of 130 genes in the domains of alcohol metabolism, stress/anxiety, monoamine function, and signaling. The array includes 186 ancestry informative markers (AIMs) genotyped in the Human Genome Diversity Panel (HGDP), enabling us to derive ancestry factor scores to rule out or correct for ethnic stratification. To facilitate use by Extramural investigators we genotyped >25,000 individuals from multiple study samples including Yale, Emory University, the Rockefeller University, Columbia University, University of Colorado, UCSD, Medical College of Virginia, Washington University, and NIDCR (Hodgkinson et al, 2008). We detected loci influencing alcoholism by whole genome linkage analysis and followed up several. At the Chr 4 GABAA subunit cluster implicated in a Plains Indian linkage scan (Long et al) linkage disequilibrium to the GABAA alpha 2 gene was found by others. We replicated this finding and showed that the association to dependence was anxiety- modulated (Enoch et al). Another GABAA gene cluster implicated in alcoholism, and alcohol response, is located on Chr 5. Within this cluster we reported linkage disequilibrium to alcoholism (Radel et al) and implicated the GABAA alpha 6 gene, where we found a missense variant associated with alcohol dependence and response to alcohol and diazepam (Iwata et al, Schuckit et al). We completed a genome scan in Plains Indians yielding genome-wide significant, or near-significant, linkage to an alcoholism-associated EEG trait, as described (AA000280-18). Intermediate phenotypes augment diagnosis by structured interview. Clinical subphenotyping enabled linkage of HTR1B to antisocial alcoholism (Lappalainen et al), serotonin transporte r (SLCA4) to anxiety (Mazzanti et al;Hariri et al), BDNF Val66Met to episodic memory (Egan et al), COMT Val158Met to anxiety (Enoch et al), executive cognition (Egan et al;Lipsky et al;Malhotra et al), and pain threshold (Zubieta et al;Diatchenko et al), and GTP cyclohydrolase to chronic pain and experimental pain response (Tegeder et al). In these studies brain imaging and cognitive measures play prominent roles. Frontal cognitive deficit is a risk factor in schizophrenia, alcoholism and other diseases. Dopamine generally enhances prefrontal cortical efficiency. Met158, a common COMT variant, leads to four-fold reduction in COMT activity. It is thus a candidate allele for cognitive function via effect on frontal dopamine. We found an allele-dosage relationship of Met158 to frontal cognitive function and diminished frontal cortical efficiency (Egan et al). The relationship to cognition is observed in populations differing in baseline cognitive function: schizophrenia, moderate-severe head injury (Lipsky et al), &controls (Malhotra et al). LNG proposed that Val158 has a counter-advantage: stress resiliency. In two populations Met158 predicted anxiety in women and decreased frontal EEG coherence (Enoch et al), and Met158 was associated with lower resiliency to pain/stress (Zubieta et al;Diatchenko et al). Met158 predicted inability to activate endomorphin release after pain/stress (Zubieta et al).Overall, effect sizes of genes in intermediate phenotypes is larger (Goldman and Ducci, 2007). Sampling framework and genetic structures enhance detection of GxE effects, to achieve greater homogeneity of genetic background and exposures, and to enrich for exposures and outcomes. A Finnish dataset was ascertained from criminal alcoholic probands &thus enriched for Type II early onset alcoholism. SW Indian, Plains Indian, &Finnish datasets are derived from isolates, with psychiatrically interviewed controls available from source populations. An African American cocaine/opioid dependence dataset N=1000 was powerful for detecting GxE of childhood adversity and HTTLPR in adult suicidality (Roy et al, 2007) because of high rates of adversity and suicidality in substance dependence. In that African-American datset, early life stress and poverty, but not African ancestry, predicted high risk of covine, opioid and alcohol addictions (Ducci et al, 2009). An MAOA functional VNTR previously linked to dyscontrol via stress interaction was linked to outcomes of alcohol dependence and ASPD in American Indian women, of whom approximately half had been sexually abused as children (Ducci et al, 2008). In the Finns, deep sequencing detected a novel Stop codon variant that is relatively common (>1%), apparently restricted to Finns (not, for example, present in the Human Genome Diversity Panel) and that is both associated with impulsive disorders (ASPD, Intermittent Explosive Disorder and Alcoholism) and co-segregating with these phenotypes in families (Bevilacqua et al, submitted). The genome-wide integrative approach is amplified by large scale genotyping enabling whole genome association, and next generation sequencing. We completed an Illumina 550k genome-wide scan for EEG variation associated with alcoholism and other psychiatric diseases and discovered independent genome-wide significant loci controlling variation in the EEG (Hodgkinson et al, submitted). Next-generation sequencing was used to analyze brain histone methylation and transcriptome changes resulting from early maternal deprivation in Rhesus macaques (Barr et al, in preparation).